Non-human microbiomes, June 5

Meta-analysis of avian gut microbiomes, mosquitos, microbes and oil-spills, and fungi and viruses found on corals and sponges.

Bird microbiome

Screen Shot 2014-06-05 at 11.23.11 AMCharacterizing the avian gut microbiota: membership, driving influences, and potential function – David W. Waite – Frontiers in Microbiology, Microbial Symbioses

“In this study, we present the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available clone-library and amplicon pyrosequencing data. “

Insect microbiome

Screen Shot 2014-06-05 at 11.24.12 AMPyrosequencing 16S rRNA genes of bacteria associated with wild tiger mosquito Aedes albopictus: a pilot study – Guillaume Minard – Frontiers in Cellular and Infection Microbiology

“We surveyed the bacteria associated with field populations of Ae. albopictus from Madagascar by pyrosequencing 16S rRNA gene amplicons. Different aspects of amplicon preparation and sequencing depth were tested to optimize the breadth of bacterial diversity identified”

Screen Shot 2014-06-05 at 11.24.56 AMMultifaceted Defense against Antagonistic Microbes in Developing Offspring of the Parasitoid Wasp Ampulex compressa (Hymenoptera, Ampulicidae) – Katharina Weiss – PLOS ONE

“Larvae of the emerald cockroach wasp, Ampulex compressa, sanitize their cockroach hosts, Periplaneta americana, with a cocktail of nine antimicrobials comprising mainly (R)-(-)-mellein and micromolide.”

Invertebrate microbiome

Screen Shot 2014-06-02 at 6.19.53 PMReview: Fungal association with sessile marine invertebrates – Oded Yarden – Frontiers in Microbiology, Microbial Symbioses

“The ecological function of fungi in association with sessile marine animals is complex and is founded on a combination of factors such as fungal origin, host health, environmental conditions and the presence of other resident or invasive microorganisms in the host.”

Screen Shot 2014-06-02 at 6.19.09 PMGenerating viral metagenomes from the coral holobiont – Karen D. Weynberg – Frontiers in Microbiology, Virology

“Here we present the first protocol for isolating, purifying and amplifying viral nucleic acids from corals based on mechanical disruption of cells. This method produces at least 50% higher yields of viral nucleic acids, has very low levels of cellular sequence contamination and captures wider viral diversity than previously used chemical-based extraction methods.”

Plant microbiome

Screen Shot 2014-06-05 at 11.26.58 AMColonization of plants by human pathogenic bacteria in the course of organic vegetable production – Andreas Hoffman – Frontiers in Microbiology, Plant-Microbe Interaction

“In this study laboratory experiments in axenic and soil systems following common practices in organic farming were conducted to identify the minimal dose needed for bacterial colonization of plants and to identify possible factors like bacterial species or serovariation, plant species or organic fertilizer types used, influencing the success of plant colonization by human pathogenic bacteria”

Water microbiome

Screen Shot 2014-06-05 at 11.28.03 AMThe polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill – Anthony D. Kappell – Frontiers in Microbiology, Aquatic Microbiology

“To investigate the Gulf Coast beach microbial community response to hydrocarbon exposure, we examined the functional gene diversity, bacterial community composition, and PAH degradation capacity of a heavily oiled and non-oiled beach following the oil exposure. “

Screen Shot 2014-06-05 at 11.36.29 AMComparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach – Ana B. Fernández – Frontiers in Microbiology, Extreme Microbiology

“We analyzed the prokaryotic community structure of a saltern pond with 21% total salts located in Isla Cristina, Huelva, Southwest Spain, close to the Atlantic ocean coast. “

Screen Shot 2014-06-05 at 11.32.42 AMConversion of crude oil to methane by a microbial consortium enriched from oil reservoir production waters – Carolina Berdugo-Clavijo – Frontiers in Microbiology, Microbial Physiology and Metabolism

“Microbial community analysis revealed that the enrichment culture was dominated by members of the genus Smithella, Methanosaeta, and Methanoculleus. However, a shift in microbial community occurred following incubation of the enrichment in the sandstone columns. “

Screen Shot 2014-06-05 at 11.33.20 AMNatural oil slicks fuel surface water microbial activities in the northern Gulf of Mexico – Kai Ziervogel – Frontiers in Microbiology, Aquatic Microbiology

“These results demonstrate that the formation of oil slicks and activities of oil-degrading bacteria result in a temporal offset of microbial cycling of organic matter, affecting food web interactions and carbon cycling in surface waters over cold seeps.”

Screen Shot 2014-06-05 at 11.34.20 AMRecoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat – Anna Hanke – Frontiers in Microbiology, Evolutionary and Genomic Microbiology

“Metagenomics, proteomics and fluorescence in situ hybridization showed that this simplified community contained both a potential sulfur oxidizing Gammaproteobacteria (at 24 ± 2% abundance) and a member of the BD1-5/SN-2 candidate phylum (at 7 ± 6% abundance). “

Deep earth microbiome

Screen Shot 2014-06-05 at 11.35.07 AMChanges in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment – Andre Mu – Frontiers in Microbiology, Terrestrial Microbiology

“This study demonstrates a successful new in situ sampling approach for detecting microbial community changes associated with an scCO2 geosequestration event.”

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Animal, plant, and environmental microbiome digest, June 2, 2014

Microbiomes of rumen, salamanders, insects, corals, sponges and soil.

Mammalian microbiome

Amphibian microbiome

Insect microbiome

  • Screen Shot 2014-06-02 at 3.19.02 PMReview: Towards an integrated understanding of gut microbiota using insects as model systems – Mathieu Pernice – Journal of Insect Physiology – we give a brief overview of the characteristics of the gut microbiota in insects in terms of low diversity but high variability at intra- and interspecific levels and we investigate some of the ecological and methodological factors that might explain such variability. “

Coral and sponge microbiome

Algae and Plant microbiome

Environmental microbiome

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